If there are more than one Boolean field formatted as Check box in a section, and if we set the last one's "Visible by default" to be not visible, this setting is not obeyed when you change the record and press save, the last Boolean field will always show even though its set to be not visible in the form.

If the Boolean fields are formatted as "Two radio buttons" or List, the system works as designed.

*No custom JavaScript is used on the form